Understandable confusion: but read our submittal policies. Editors are allowed some freedom to add subpages in exceptional cases, but our policy asks people to submit sites just once.
As for: "This section of the site is not all to visible from the main part of the website."
Look at this from our standpoint. It's like saying, "I created these pages, but I don't want to ruin my reputation by linking to them from my other pages. Here -- YOU do it!"
If that section of the site is not worth giving prominent visibility from your own website, that's plenty good enough proof that it's not worth linking from ours.
And ... if it is linked from your website, it doesn't need to be linked from ours.
Think of it this way: If that section is worth surfing, and it is linked from your website, it makes your website bigger and more worth listing. It might even be what makes the difference in listing your website at all.